{"push_id":1482324331,"size":185,"distinct_size":43,"ref":"refs/heads/hotfix","head":"15ca359678895db259f2f65e46f3a0b7254320a1","before":"af147d32380339b8cc7dc09f6e9ee311ffabb128","commits":[{"sha":"0e7c4beff12c1d6dc0598adba0ef4f608fe83343","author":{"name":"Chris Wakefield","email":"56169e422ba404c4a9eadc7e15e6d6c6e20c26d9@mdanderson.org"},"message":"Add tab for MDACC Heatmap viewer on study page\n\nThis adds a new tab to the study view page.  Clicking on the tab\ndisplays an embedded \"MDACC Clustered Heatmap Compendium\" page, that\nshows only heatmaps that were indexed as belonging with the study being\nviewed.  If the user clicks on a heatmap, The NG-CHM viewer is displayed\nwithin that embedded iframe.  The approach used (the embedded iframe)\nfollows the approach for the existing embedded Digital Slide Archive\nviewer.\n\nThis is based on the 7/5/16 phone discussion with Niki Schultz, Ethan\nCerami, John Weinstein, and myself, when we demoed a patient view\nversion of the same.\n\nThe heatmap index mentioned above is queried via a web service running\nat MD Anderson, whose URL is set in the property\nmdacc.heatmap.study.meta.url in portal.properties.EXAMPLE.  A blank or\nmissing url property causes the query to be skipped and disables the\nentire functionality.  For development purposes, the test study in the\n\"Seed Database\" with id 'study_es_0' is mapped to the same heatmaps\nthat we have for study id 'brca_tcga_pub' that contains similar\nsamples.\n\nSigned-off-by: Chris Wakefield <cwakefield@mdanderson.org>","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/0e7c4beff12c1d6dc0598adba0ef4f608fe83343"},{"sha":"b1b2e2f84dc9c5d2b2d833f525348a66cc7deb16","author":{"name":"Chris Wakefield","email":"56169e422ba404c4a9eadc7e15e6d6c6e20c26d9@mdanderson.org"},"message":"Remove legacy/debug code in js file per zhx828\n\nSigned-off-by: Chris Wakefield <cwakefield@mdanderson.org>","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/b1b2e2f84dc9c5d2b2d833f525348a66cc7deb16"},{"sha":"181a1088dd237346febbc476a84c6eccfbed73c1","author":{"name":"JJ Gao","email":"a36f8b2c2e96470c39979df26ffa731a02b5510a@gmail.com"},"message":"v1.4.0-SNAPSHOT","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/181a1088dd237346febbc476a84c6eccfbed73c1"},{"sha":"0e4348f709912cbb2ff143134d5706e8dd562f16","author":{"name":"JianJiong Gao","email":"a36f8b2c2e96470c39979df26ffa731a02b5510a@gmail.com"},"message":"Merge pull request #1567 from thehyve/add_validation_scenarios\n\nAdd validation for clinical attrs with set meanings","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/0e4348f709912cbb2ff143134d5706e8dd562f16"},{"sha":"a6f8465756d83493125e2898fae3b9dabb880421","author":{"name":"JianJiong Gao","email":"a36f8b2c2e96470c39979df26ffa731a02b5510a@gmail.com"},"message":"Merge pull request #1789 from cBioPortal/hotfix\n\nHotfix to rc","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/a6f8465756d83493125e2898fae3b9dabb880421"},{"sha":"05744225a89c1f126cbeefd87347418b6b3d71d2","author":{"name":"Ersin Ciftci","email":"3ba64933e60c43ced59b5ba9f0f299b9d3702dce@jimmy.harvard.com"},"message":"Implemented 4 APIs in Clinical Data with persistence, service and web tests","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/05744225a89c1f126cbeefd87347418b6b3d71d2"},{"sha":"e7e6cd7d4c285279c5d21f5bdec0bbd5acfd6d70","author":{"name":"Robert Sheridan","email":"330f20dd7a05df2f39e3b4018cd9de64eb8d46b0@cbio.mskcc.org"},"message":"Merge pull request #1743 from ersinciftci/clinical-data\n\nImplemented 4 APIs in Clinical Data with persistence, service and web tests","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/e7e6cd7d4c285279c5d21f5bdec0bbd5acfd6d70"},{"sha":"cece947a531fbb8a29ed32e8129d63519a5be8ff","author":{"name":"Robert Sheridan","email":"330f20dd7a05df2f39e3b4018cd9de64eb8d46b0@cbio.mskcc.org"},"message":"Bugfix (1799) : migration.sql\n- move ALTER TABLE line beneath a needed CREATE TABLE line","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/cece947a531fbb8a29ed32e8129d63519a5be8ff"},{"sha":"a302db5913bfcdce3f7bc6d24d8f46080253ecb1","author":{"name":"Sun","email":"9fc24398564f7fb923d9334db9cf63759c1a2302@lski1780.mskcc.org"},"message":"issue #1792","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/a302db5913bfcdce3f7bc6d24d8f46080253ecb1"},{"sha":"189d72e995abc7490f8177f01f0b276256e7ce0b","author":{"name":"zheins","email":"3373aced974f1186d480abd327ca45b749d28b59@gmail.com"},"message":"Gene panel api expansion for oncoprint","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/189d72e995abc7490f8177f01f0b276256e7ce0b"},{"sha":"8684766dfd28cf4dd24445e4ea46fa7c7c6b5f87","author":{"name":"Robert Sheridan","email":"330f20dd7a05df2f39e3b4018cd9de64eb8d46b0@cbio.mskcc.org"},"message":"Merge pull request #1734 from zheins/gp-oncoprint-backend\n\nqueries are now by profile and gene set. If a sample has no gene panel (all exon sequenced) it is not present in the response. The response is a set of gene panels, each one contains a list of genes which intersect with the queried genes (parameter) and the list of samples processed using the panel. Also, if a set of queried genes is completely disjoint with the gene panel set of genes, the API reports the panel used (name + description) with an empty set of genes in the intersection.","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/8684766dfd28cf4dd24445e4ea46fa7c7c6b5f87"},{"sha":"12d2654f3865dd01de0a1831f30071f91559a6ea","author":{"name":"n1zea144","email":"97a66092c248ebb1337e10009a61139f39ce5961@gmail.com"},"message":"Removed files from original #1584 PR that should not get pushed\nBug fixes to original SV branch","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/12d2654f3865dd01de0a1831f30071f91559a6ea"},{"sha":"e6f82b812a99dfd77e093217feb5917afcdd717f","author":{"name":"Robert Sheridan","email":"330f20dd7a05df2f39e3b4018cd9de64eb8d46b0@cbio.mskcc.org"},"message":"Made unit tests work, refactored and renamed code (StructuralVariant)\n-add copyright/license to top of all involved files\n-reordered table drop statements to drop child tables before parents\n-altered sv table sample field mapping to use internal_id (not stable). gene still uses hugo gene name\n-int sv table, changed some data types to be sensible (not int(255))\n-renamed classes with \"SV\" to have \"StructuralVariant\"\n-renamed db table \"sv\" to \"structural_variant\"\n-set api endpoint to \"structuralvariant\" from \"sv\"\n-put controller into subpackage : org.cbioportal.web.legacy\n-controller test class moved to a parallel package path\n-dropped insert functionality from mybatis mapper and service layer\n-added additional unit tests for repository\n-corrected logical operator precidence problem in mapper\n-style changes: drop tab characters and standardize indents (4 - java, 2 - xml)\n-added additional records to test data database construction script\n-reduce controller level tests : one \"full\" mock object and one empty (to test proper json formatting)\n-changed GeneticProfileType to enum class (with lookup by string value)\n-added adjustments to cgds.sql, migration.sql, seed_mini.sql, testSql.sql [appropriate schema/test data]\n-adjusted foreign key in cgds.sql (to internal)","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/e6f82b812a99dfd77e093217feb5917afcdd717f"},{"sha":"6146e33c885300b07636006db0a7d05ee419395b","author":{"name":"Sun","email":"9fc24398564f7fb923d9334db9cf63759c1a2302@lski1780.mskcc.org"},"message":"Merge branch 'rc' into zscore-dev","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/6146e33c885300b07636006db0a7d05ee419395b"},{"sha":"c183ab2f1f20aea976ab01bd303c60c0ff1930ce","author":{"name":"Sun","email":"9fc24398564f7fb923d9334db9cf63759c1a2302@lski1780.mskcc.org"},"message":"hide the testing print lines","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/c183ab2f1f20aea976ab01bd303c60c0ff1930ce"},{"sha":"4366a95320e0cbd17cd0ac9ad5f1a7ce3dfaa0eb","author":{"name":"n1zea144","email":"97a66092c248ebb1337e10009a61139f39ce5961@gmail.com"},"message":"Merge pull request #1648 from sheridancbio/jake-structural-variant-pull-fixed-rc\n\nStructural Variant model / persistence / controller + unit tests & refactoring","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/4366a95320e0cbd17cd0ac9ad5f1a7ce3dfaa0eb"},{"sha":"a6a20b79610635a500a8e657b0ab5b79dad0f9fd","author":{"name":"Ersin Ciftci","email":"3ba64933e60c43ced59b5ba9f0f299b9d3702dce@jimmy.harvard.com"},"message":"Implemented 2 endpoints in Study API with persistence, service and web tests\n\nGET /studies\nGET /studies/{studyId}","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/a6a20b79610635a500a8e657b0ab5b79dad0f9fd"},{"sha":"10545384311d074bfa86c3a43babcfd3a494cdc2","author":{"name":"Robert Sheridan","email":"330f20dd7a05df2f39e3b4018cd9de64eb8d46b0@cbio.mskcc.org"},"message":"correct comment syntax in mysql scripts","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/10545384311d074bfa86c3a43babcfd3a494cdc2"},{"sha":"a1537f4e24ffd3f3a79e44623b4aa33286cf0a2d","author":{"name":"Robert Sheridan","email":"330f20dd7a05df2f39e3b4018cd9de64eb8d46b0@cbio.mskcc.org"},"message":"Fix comment syntax errors in sql files\n- also drop duplicated license banner","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/a1537f4e24ffd3f3a79e44623b4aa33286cf0a2d"},{"sha":"9edf0f8b9d62aafffe8a1df45fbfa5967d06e98f","author":{"name":"n1zea144","email":"97a66092c248ebb1337e10009a61139f39ce5961@gmail.com"},"message":"Merge pull request #1823 from sheridancbio/rc\n\ncorrect comment syntax in sql files","distinct":false,"url":"https://api.github.com/repos/zhx828/cbioportal/commits/9edf0f8b9d62aafffe8a1df45fbfa5967d06e98f"}]}
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